Update: this is an answer to the wrong question! It solves the problem of quoting only the first and last n/N runs. The OP wants to replace the first and last N/n in each run with ^.

The following (rather fussy because of special cases) code remembers where the last N/n run started then rewrites the last part of the output file with the markers inserted.

use strict;
use warnings;

my $data = <<DATA;
acacccacacacaccacacccacacaccacacccacacccacacaccaca
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaacccnnnnnnnnnnnnnnnnnnnnnnnnnnnccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
ggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnaccctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
DATA

my $result;

open my $inFile,  '<', \$data or die "Unable to open input fille: $!\n
+";
open my $outFile, '>', \$result or die "Unable to create output file: 
+$1\n";

my $currStartN;
my $lastStartN;
my $lastEndN;
my $prevLineEnd = 0;

while (<$inFile>) {
    my $runEnd;

    if (defined $currStartN) {
        # Looking for an end N/n
        next unless /([^nN\n])/; # Continue if full line of N/n

        $runEnd = $-[0];
        # Insert ^ for first run
        if ($runEnd == 0) {
            # Need to insert ^ at end of previous line
            seek $outFile, $prevLineEnd, 0;
            print $outFile "^\n";
        } else {
            substr $_, $runEnd, 0, '^' unless defined $lastStartN;
        }

    } else {
        # Looking for a start N/n
        next unless /([nN]+)/;

        $runEnd = $+[0];
        $currStartN = tell ($inFile) - length ($_) + $-[0];
        s/([nN])/^$1/ unless defined $lastStartN; # Insert ^ for first
+ run
        next unless $runEnd < length ($_) - 2; # Continue if full line
+ of N/n
    }

    $lastStartN = $currStartN;
    $lastEndN = tell ($inFile) - length ($_) + $runEnd;
    $currStartN = undef;

} continue {
    $prevLineEnd = tell $outFile;
    print $outFile $_;
    chomp;
    $prevLineEnd += length;
}

# Insert ^ around last run of N/n
seek $outFile, $lastStartN + 2, 0;
print $outFile '^';

seek $inFile, $lastStartN, 0;
read $inFile, my $nRun, ($lastEndN - $lastStartN - 1);
print $outFile $nRun, '^';
print $outFile $_ while <$inFile>;

close $inFile;
close $outFile;

print $result;
[download]

Prints:

acacccacacacaccacacccacacaccacacccacacccacacaccaca
^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn^
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaacccnnnnnnnnnnnnnnnnnnnnnnnnnnnccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
gg^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnn^naccctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
[download]